Over the next several lab periods, we will be building a model of Gramicidin A embedded in a lipid bilayer with surrounding solvent, running molecular dynamics, and analyzing these simulations to explore the biophysical properties of the system.
Part I Model Building
Part II Minimization and Equilibration
Part III Analysis
NOTE: The protocols described in this tutorial are for educational purposes only and have been modified to fit within the time constraints of the hands-on lab sessions. Therefore they do not necessarily represent simulation best practices and care should be taken if translating them into a production environment.